Just to ressurect an old thread and to update things, I've dumped the idea of using Calibre and iTunes to copy books to the iPad's Kindle app, or indeed, iBooks, which I've removed from the device.

For large PDFs I use iTunes directly and the file sharing feature under "Apps". For recipes I've discovered and worked out the "Connect-Share/Send via email" function. I'm also using that to send proper books to the cloud using my kindle.com email address linked to one of the Kindles.

From there it's a simple matter of getting the device and telling it to download the books/recipes as required.

I haven't done much with my Kindle/Kindle apps since I first started this thread. But my interest was rekindled (pun intended) when my wife got me a Kindle Paperwhite for Christmas.